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Detailed information for vg0819068671:

Variant ID: vg0819068671 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19068671
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

ACTCACCTAGCATATGCTTAGCCAAATTGATTCACCAAAATACTAAATTGTCAAGTTCTTGTATTAGAACGCACCCACTTGTCAAGTTGTTGCACTCGGA[C/T]
ATTCAATTCTCAAGTTCTTGCACTATATCGCACCCACCTGCCGATAGGGGTGGAAACGAGCCAAGCCGAGCCGAGCTCGGCTTCGTGAAAGCTTGGTCAA

Reverse complement sequence

TTGACCAAGCTTTCACGAAGCCGAGCTCGGCTCGGCTTGGCTCGTTTCCACCCCTATCGGCAGGTGGGTGCGATATAGTGCAAGAACTTGAGAATTGAAT[G/A]
TCCGAGTGCAACAACTTGACAAGTGGGTGCGTTCTAATACAAGAACTTGACAATTTAGTATTTTGGTGAATCAATTTGGCTAAGCATATGCTAGGTGAGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.80%	31.70%	1.44%	0.00%	NA
All Indica	2759	45.00%	52.60%	2.39%	0.00%	NA
All Japonica	1512	98.70%	1.30%	0.07%	0.00%	NA
Aus	269	98.50%	1.10%	0.37%	0.00%	NA
Indica I	595	26.40%	71.40%	2.18%	0.00%	NA
Indica II	465	17.00%	79.40%	3.66%	0.00%	NA
Indica III	913	63.20%	35.40%	1.42%	0.00%	NA
Indica Intermediate	786	54.50%	42.60%	2.93%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	97.80%	2.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819068671	C -> T	LOC_Os08g30900.1	upstream_gene_variant ; 1869.0bp to feature; MODIFIER	silent_mutation	Average:53.75; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0819068671	C -> T	LOC_Os08g30900.2	upstream_gene_variant ; 2358.0bp to feature; MODIFIER	silent_mutation	Average:53.75; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0819068671	C -> T	LOC_Os08g30870-LOC_Os08g30900	intergenic_region ; MODIFIER	silent_mutation	Average:53.75; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819068671	NA	6.65E-09	mr1457	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0819068671	NA	1.81E-07	mr1707	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0819068671	3.89E-06	7.03E-11	mr1707_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0819068671	NA	6.86E-11	mr1728_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251